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- PDB-2ow4: Crystal structure of a lectin from Canavalia maritima seeds (ConM... -

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Basic information

Entry
Database: PDB / ID: 2ow4
TitleCrystal structure of a lectin from Canavalia maritima seeds (ConM) in complex with man1-2man-OMe
ComponentsCanavalia maritima lectin
KeywordsSUGAR BINDING PROTEIN / Canavalia maritima / lectin / man1-2man-OMe
Function / homology
Function and homology information


D-mannose binding / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia maritima (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMoreno, F.B.M.B. / Bezerra, G.A. / de Oliveira, T.M. / de Souza, E.M. / da Rocha, B.A.M. / Benevides, R.G. / Delatorre, P. / Cavada, B.S. / de Azevedo Jr., W.F.
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure-biological activity ...Title: Structural analysis of Canavalia maritima and Canavalia gladiata lectins complexed with different dimannosides: New insights into the understanding of the structure-biological activity relationship in legume lectins.
Authors: Bezerra, G.A. / Oliveira, T.M. / Moreno, F.B. / de Souza, E.P. / da Rocha, B.A. / Benevides, R.G. / Delatorre, P. / de Azevedo, W.F. / Cavada, B.S.
History
DepositionFeb 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence the sequence is not available in uniprot database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Canavalia maritima lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9334
Polymers25,4821
Non-polymers4513
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Canavalia maritima lectin
hetero molecules

A: Canavalia maritima lectin
hetero molecules

A: Canavalia maritima lectin
hetero molecules

A: Canavalia maritima lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,73416
Polymers101,9294
Non-polymers1,80512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area12510 Å2
ΔGint-96 kcal/mol
Surface area31010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.252, 89.094, 85.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Canavalia maritima lectin


Mass: 25482.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: seed protein / Source: (natural) Canavalia maritima (plant) / References: UniProt: P81364
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.4
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Apr 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 1.4→22.82 Å / Num. obs: 30905 / % possible obs: 25 % / Redundancy: 4 % / Rmerge(I) obs: 0.055 / Rsym value: 5.5 / Net I/σ(I): 15.5
Reflection shellResolution: 1.4→1.641 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 2.4 / Rsym value: 45.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→22.82 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.579 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23039 1646 5.1 %RANDOM
Rwork0.20645 ---
obs0.20769 30905 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.826 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1800 0 26 135 1961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211865
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9412542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4985235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57624.80577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40215286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.245156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021395
X-RAY DIFFRACTIONr_nbd_refined0.2330.21065
X-RAY DIFFRACTIONr_nbtor_refined0.320.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2192
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.220
X-RAY DIFFRACTIONr_mcbond_it0.8311.51182
X-RAY DIFFRACTIONr_mcangle_it1.47221902
X-RAY DIFFRACTIONr_scbond_it2.163749
X-RAY DIFFRACTIONr_scangle_it3.3514.5640
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 106 -
Rwork0.305 2223 -
obs--97.86 %

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